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Robust Automated Truncation Point Selection for Molecular Simulations

Lookup NU author(s): Dr Daniel ColeORCiD

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

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Author(s): Clark F, Cole DJ, Michel J

Publication type: Article

Publication status: Published

Journal: Journal of Chemical Theory and Computation

Year: 2024

Volume: 21

Issue: 1

Pages: 88-101

Online publication date: 23/12/2024

Acceptance date: 09/12/2024

Date deposited: 15/01/2025

ISSN (print): 1549-9618

ISSN (electronic): 1549-9626

Publisher: American Chemical Society

URL: https://doi.org/10.1021/acs.jctc.4c01359

DOI: 10.1021/acs.jctc.4c01359

Data Access Statement: All methods were implemented in the open-source Python package RED (robust equilibration detection, where equilibration is used in the sense of finding the optimal truncation point) available from the PyPI, conda-forge, and at github.com/fjclark/red. A complete workflow to reproduce the study beginning from the absolute binding free energy gradient data is provided at github.com/michellab/Robust-Equilibration-Detection-Paper and all data are provided on Zenodo. (51)

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